I was recently on a transatlantic fight which was 4 hours delayed. Needless to say, everyone iwth a connection missed it, and all of those people were going to be processed at the transfer desk. Luckily, being Elite I had select seating towards the front of coach and was the second passenger from the flight to make it to the transfer desk and I did not have to wait at all. Needless to say the folks at the back of the plane did not fair as well.

Question: Is there away, assuming elite status and perhaps assuming lounge access, to avoid the transfer desk? Alternatives that come to mind would be the Crown Lounge or passing through customs and going to the regular check-in counter. Presumably the check-in counter could give a boarding pass if you had already been automatically re-booked, but could the check-in desk help if you had not?

What I've done in similair situations is to go to another transfer desk. If my schengen flight was late I pass through the passport control to the non-schengen transfer desk with hopefully less queues, and vice versa.

There are several transfer desks; you should be able to use any of them. The LoungeDragons may also be able to help you. The last time I used a transfer desk there was an elite line, also. Funny story: there was a very nice young lady helping me there and a guy came up to the counter next to me and asked if this is where he needs to be for a missed connection. She positively roared at him that she was busy with a customer, couldn't he see that, and to go wait in that line over there (indicating the regular, non-elite line full of people waiting). Then she looked up at me and smiled, and handed me my boarding pass.

The agents in the lounges have only limited access to the reservation system, so if you need to be rebooked and your original reservation has to be changed / modified, you still need to use the transfer desks, which are normally overcrowded.

I do not know if that has changed lately and I was in fact served by them as well ( i.e rebooked on the train once ) but was also told to pick the train tix at the station, so there was hardly any consistency...

There is one transfer deck close to the Museum, a little bit hidden, which used to have shorter lines...

I think that one is actually a ticket desk, not a transfer desk. Should still be able to assist with transfer issues.

Johan